Targeting Wnt/β-catenin and circadian regulator restores PRC2/EZH2-controlled chromatin bivalency and suppresses cell state diversity
Yatian Yang, Xiong Zhang, Varadha Balaji Venkadakrishnan, Hongye Zou, Xingling Zheng, Shiyao Guo, Christopher Z. Chen, Alexander D. Borowsky, Eva Corey, Ronald M. Evans, Allen C. Gao, Marc A. Dall’Era, Amina Zoubeidi, Primo N. Lara, Hsing-Jien Kung, Xinbin Chen, Himisha Beltran, Hong-Wu Chen
Yatian Yang, Xiong Zhang, Varadha Balaji Venkadakrishnan, Hongye Zou, Xingling Zheng, Shiyao Guo, Christopher Z. Chen, Alexander D. Borowsky, Eva Corey, Ronald M. Evans, Allen C. Gao, Marc A. Dall’Era, Amina Zoubeidi, Primo N. Lara, Hsing-Jien Kung, Xinbin Chen, Himisha Beltran, Hong-Wu Chen
View: Text | PDF
Research Article Cell biology Genetics Oncology

Targeting Wnt/β-catenin and circadian regulator restores PRC2/EZH2-controlled chromatin bivalency and suppresses cell state diversity

Abstract

PRC2/EZH2 inhibitors (PRC2i/EZH2i) are promising for the treatment of advanced cancers including metastatic prostate cancer. Here, we show that PRC2i/EZH2i alone or in combination with androgen receptor (AR) inhibitors induced diverse cell state programs (CSPs) (e.g., response to stress or IFN, MYC targets, stem cells, EMT lineage plasticity, and multiple developmental programs), which led to increased tumor cell invasion, metastasis, and resistance to other drugs, in addition to modest suppression of tumor growth. In contrast to the current perception, our comprehensive, integrated genomics and epigenomics profiling of patient-derived xenografts (PDXs) and clinical tumors revealed that PRC2/EZH2 suppressed CSP genes by maintaining chromatin bivalency. Hyperactive Wnt/β-catenin signaling and inhibitors of polycomb-repressive complex 2/enhancer of zeste homolog 2 (PRC2/EZH2) and the AR alter chromatin bivalency through antagonism of PRC2 and stimulation of MLL2/KMT2B in a feed-forward manner. The circadian rhythm regulator REV-ERBα unexpectedly reprogrammed β-catenin in promoting bivalency resolution and CSP gene expression. Dual targeting of Wnt/β-catenin and EZH2 diminished diverse cell states by restoring bivalency and effectively blocked tumor growth. Our findings provide unexpected insights into chromatin bivalency and dysregulated circadian rhythms in the control of cell state diversity and identify alternative therapeutic strategies that target PRC2/EZH2 for advanced malignancies.

Authors

Yatian Yang, Xiong Zhang, Varadha Balaji Venkadakrishnan, Hongye Zou, Xingling Zheng, Shiyao Guo, Christopher Z. Chen, Alexander D. Borowsky, Eva Corey, Ronald M. Evans, Allen C. Gao, Marc A. Dall’Era, Amina Zoubeidi, Primo N. Lara, Hsing-Jien Kung, Xinbin Chen, Himisha Beltran, Hong-Wu Chen

×

Figure 3

Induction of cell state diversity is associated with alteration of chromatin bivalency.

Options: View larger image (or click on image) Download as PowerPoint
Induction of cell state diversity is associated with alteration of chrom...
(A) Venn diagram of overlapping genes (n = 2,945) among 3,276 genes, with peaks detected by H3K27me3 to H3K4me3 sequential ChIP-seq (green) and among 3,372 genes, with peaks detected by H3K4me3 and H3K27me3 separate ChIP-seq (blue) in LuCaP77EnzR PDX tumors. (B) Number of bivalent genes identified in the indicated models and in fresh human tumors. (C) Integrative Genomic Viewer (IGV) snapshots of sequential or separate ChIP-seq of H3K27me3 and H3K4me3 at representative CSP genes in C4-2B cells, LuCaP77EnzR PDX tumors, and fresh human tumors. (D) Venn diagram of overlapping genes (n = 856) among bivalent genes in all models and cell state genes and bar plot of major programs from GO analysis. (E) Pie charts of the percentage of bivalent and nonbivalent genes upregulated by Taz and Enz combination treatment in the indicated models. (F) K-means analysis of bivalent promoters and heatmaps of H3K4me3 and H3K27me3 ChIP-seq signal intensity within ±3 kb windows around the TSS at cluster I (H3K4me3-high, with intensity of H3K4me3 higher than H3K27me3 FC ≥1.5), cluster II (H3K27me3-high, with intensity of H3K27me3 higher than H3K4me3 FC ≥1.5), and cluster III (H3K4me3/K27me3-equal, with intensity of H3K27me3 equal to that of H3K4me3 |FC|<1.5 in the indicated models. (G) Alluvial plot of dynamic changes of chromatin bivalency states (CBSs) in the 3 clusters from drug-sensitive cells (LNCaP) to drug-resistant cells (42DEnzR). (H) IGV snapshots of H3K27me3 and H3K4me3 ChIP-seq at a representative gene in the indicated cells and PDX models. (I) Scatter plot of log2 FC in H3K4me3 mark intensity between 42DEnzR and LNCaP cells at all bivalent promoters and log2 FC in bivalent gene transcript levels between 42DEnzR and LNCaP cells. Pearson’s correlation scores and associated P value are indicated.